Expression Profile of Genes from 12P in Testicular Germ Cell Tumors Of
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Enhanced Representation of Natural Product Metabolism in Uniprotkb
H OH metabolites OH Article Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB Marc Feuermann 1,* , Emmanuel Boutet 1,* , Anne Morgat 1 , Kristian B. Axelsen 1, Parit Bansal 1, Jerven Bolleman 1 , Edouard de Castro 1, Elisabeth Coudert 1, Elisabeth Gasteiger 1,Sébastien Géhant 1, Damien Lieberherr 1, Thierry Lombardot 1,†, Teresa B. Neto 1, Ivo Pedruzzi 1, Sylvain Poux 1, Monica Pozzato 1, Nicole Redaschi 1 , Alan Bridge 1 and on behalf of the UniProt Consortium 1,2,3,4,‡ 1 Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel-Servet, CH-1211 Geneva 4, Switzerland; [email protected] (A.M.); [email protected] (K.B.A.); [email protected] (P.B.); [email protected] (J.B.); [email protected] (E.d.C.); [email protected] (E.C.); [email protected] (E.G.); [email protected] (S.G.); [email protected] (D.L.); [email protected] (T.L.); [email protected] (T.B.N.); [email protected] (I.P.); [email protected] (S.P.); [email protected] (M.P.); [email protected] (N.R.); [email protected] (A.B.); [email protected] (U.C.) 2 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 3 Protein Information Resource, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE 19711, USA 4 Protein Information Resource, Georgetown University Medical Center, 3300 Whitehaven Street NorthWest, Suite 1200, Washington, DC 20007, USA * Correspondence: [email protected] (M.F.); [email protected] (E.B.); Tel.: +41-22-379-58-75 (M.F.); +41-22-379-49-10 (E.B.) † Current address: Centre Informatique, Division Calcul et Soutien à la Recherche, University of Lausanne, CH-1015 Lausanne, Switzerland. -
Research Resources for Nuclear Receptor Signaling Pathways Neil J
Molecular Pharmacology Fast Forward. Published on May 23, 2016 as DOI: 10.1124/mol.116.103713 This article has not been copyedited and formatted. The final version may differ from this version. MOL #103713 Research resources for nuclear receptor signaling pathways Neil J. McKenna Department of Molecular and Cellular Biology and Nuclear Receptor Signaling Atlas (NURSA) Bioinformatics Resource, Downloaded from Baylor College of Medicine, Houston, TX, 77030, USA molpharm.aspetjournals.org at ASPET Journals on September 27, 2021 1 Molecular Pharmacology Fast Forward. Published on May 23, 2016 as DOI: 10.1124/mol.116.103713 This article has not been copyedited and formatted. The final version may differ from this version. MOL #103713 Running title: Research resources for NR signaling pathways Corresponding author: Neil J McKenna Room M620 Baylor College of Medicine One Baylor Plaza Downloaded from Houston, TX, 77030, USA t: 713-798-7490 molpharm.aspetjournals.org f: 713-798-6822 e: [email protected] Number of text pages: 21 at ASPET Journals on September 27, 2021 Number of tables: 1 Number of figures: 1 Number of references: 56 Number of words in Abstract: 124 Review: 3613 List of non-standard abbreviations: 17βE2, 17β-estradiol; AB, Allen Brain Atlas; BG, BIOGRID; BGS, BioGPS; CoR, coregulator; CTD, Comparative Toxicogenomics Database; DAV, DAVID; DB, DrugBank; EDC, endocrine disrupting chemical; EG, Entrez Gene; EM, Edinburgh Mouse; ENC, ENCODE; ENR, ENRICHR; ENS, Ensembl; EX, Expression Atlas; GC, GeneCards; GSEA, GeneSet Enrichment Analysis; GtoP, IUPHAR Guide To Pharmacology; 2 Molecular Pharmacology Fast Forward. Published on May 23, 2016 as DOI: 10.1124/mol.116.103713 This article has not been copyedited and formatted. -
Uniprot: the Universal Protein Knowledgebase in 2021 the Uniprot Consortium1,2,3,4,*
D480–D489 Nucleic Acids Research, 2021, Vol. 49, Database issue Published online 25 November 2020 doi: 10.1093/nar/gkaa1100 UniProt: the universal protein knowledgebase in 2021 The UniProt Consortium1,2,3,4,* 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK, 2Protein Information Resource, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC 20007, USA, 3Protein Information Resource, University of Delaware, Ammon-Pinizzotto Biopharmaceutical Innovation Building, Suite 147, 590 Avenue 1743, Newark, DE 19713, USA and 4SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland Received September 15, 2020; Revised October 21, 2020; Editorial Decision October 22, 2020; Accepted November 02, 2020 ABSTRACT tomated systems. The UniRef databases cluster sequence sets at various levels of sequence identity and the UniProt The aim of the UniProt Knowledgebase is to provide Archive (UniParc) delivers a complete set of known se- users with a comprehensive, high-quality and freely quences, including historical obsolete sequences. UniProt accessible set of protein sequences annotated with additionally integrates, interprets, and standardizes data functional information. In this article, we describe from multiple selected resources to add biological knowl- significant updates that we have made over the last edge and associated metadata to protein records and acts two years to the resource. The number of sequences as a central hub from which users can link out to 180 in UniProtKB has risen to approximately 190 million, other resources. In recognition of the quality of our data, despite continued work to reduce sequence redun- and the service we provide, UniProt was recognised as dancy at the proteome level. -
The Chromosome-Centric Human Proteome Project for Cataloging Proteins Encoded in the Genome
CORRESPONDENCE The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome To the Editor: utility for biological and disease studies. Table 1 Features of salient genes on The Chromosome-Centric Human With development of new tools for in- chromosomes 13 and 17 Proteome Project (C-HPP) aims to define depth characterization of the transcriptome Genea AST nsSNPs the full set of proteins encoded in each and proteome, the HPP is well positioned Chromosome 13 chromosome through development of a to have a strategic role in addressing the BRCA2 3 54 standardized approach for analyzing the complexity of human phenotypes. With this RB1 2 3 massive proteomic data sets currently being in mind, the HUPO has organized national IRS2 1 3 generated from dedicated efforts of national chromosome teams that will collaborate and international teams. The initial goal with well-established laboratories building Chromosome 17 of the C-HPP is to identify at least one complementary proteotypic peptides, BRCA1 24 24 representative protein encoded by each of antibodies and informatics resources. ERBB2 6 13 the approximately 20,300 human genes1,2. An important C-HPP goal is to encourage TP53 14 5 aEnsembl protein and AST information can be found at The proteins will be characterized for tissue capture and open sharing of proteomic http://www.ensembl.org/Homo_sapiens/. localization and major isoforms, including data sets from diverse samples to enhance AST, alternative splicing transcript; nsSNP, nonsyno- mous single-nucleotide polyphorphism assembled from post-translational modifications (PTMs), a gene- and chromosome-centric display data from the 1000 Genomes Projects. -
Rna-Sequencing Applications: Gene Expression Quantification and Methylator Phenotype Identification
The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 8-2013 RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION Guoshuai Cai Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Bioinformatics Commons, Computational Biology Commons, and the Medicine and Health Sciences Commons Recommended Citation Cai, Guoshuai, "RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION" (2013). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 386. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/386 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION -
Genomic and Transcriptome Analysis Revealing an Oncogenic Functional Module in Meningiomas
Neurosurg Focus 35 (6):E3, 2013 ©AANS, 2013 Genomic and transcriptome analysis revealing an oncogenic functional module in meningiomas XIAO CHANG, PH.D.,1 LINGLING SHI, PH.D.,2 FAN GAO, PH.D.,1 JONATHAN RUssIN, M.D.,3 LIYUN ZENG, PH.D.,1 SHUHAN HE, B.S.,3 THOMAS C. CHEN, M.D.,3 STEVEN L. GIANNOTTA, M.D.,3 DANIEL J. WEISENBERGER, PH.D.,4 GAbrIEL ZADA, M.D.,3 KAI WANG, PH.D.,1,5,6 AND WIllIAM J. MAck, M.D.1,3 1Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California; 2GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China; 3Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, California; 4USC Epigenome Center, Keck School of Medicine, University of Southern California, Los Angeles, California; 5Department of Psychiatry, Keck School of Medicine, University of Southern California, Los Angeles, California; and 6Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California Object. Meningiomas are among the most common primary adult brain tumors. Although typically benign, roughly 2%–5% display malignant pathological features. The key molecular pathways involved in malignant trans- formation remain to be determined. Methods. Illumina expression microarrays were used to assess gene expression levels, and Illumina single- nucleotide polymorphism arrays were used to identify copy number variants in benign, atypical, and malignant me- ningiomas (19 tumors, including 4 malignant ones). The authors also reanalyzed 2 expression data sets generated on Affymetrix microarrays (n = 68, including 6 malignant ones; n = 56, including 3 malignant ones). -
Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024
Document downloaded from http://www.elsevier.es, day 26/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Nº Ref Uniprot Proteína Péptidos identificados 1 P01024 CO3_HUMAN Complement C3 OS=Homo sapiens GN=C3 PE=1 SV=2 por 162MS/MS 2 P02751 FINC_HUMAN Fibronectin OS=Homo sapiens GN=FN1 PE=1 SV=4 131 3 P01023 A2MG_HUMAN Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 128 4 P0C0L4 CO4A_HUMAN Complement C4-A OS=Homo sapiens GN=C4A PE=1 SV=1 95 5 P04275 VWF_HUMAN von Willebrand factor OS=Homo sapiens GN=VWF PE=1 SV=4 81 6 P02675 FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 78 7 P01031 CO5_HUMAN Complement C5 OS=Homo sapiens GN=C5 PE=1 SV=4 66 8 P02768 ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 66 9 P00450 CERU_HUMAN Ceruloplasmin OS=Homo sapiens GN=CP PE=1 SV=1 64 10 P02671 FIBA_HUMAN Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 58 11 P08603 CFAH_HUMAN Complement factor H OS=Homo sapiens GN=CFH PE=1 SV=4 56 12 P02787 TRFE_HUMAN Serotransferrin OS=Homo sapiens GN=TF PE=1 SV=3 54 13 P00747 PLMN_HUMAN Plasminogen OS=Homo sapiens GN=PLG PE=1 SV=2 48 14 P02679 FIBG_HUMAN Fibrinogen gamma chain OS=Homo sapiens GN=FGG PE=1 SV=3 47 15 P01871 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 SV=3 41 16 P04003 C4BPA_HUMAN C4b-binding protein alpha chain OS=Homo sapiens GN=C4BPA PE=1 SV=2 37 17 Q9Y6R7 FCGBP_HUMAN IgGFc-binding protein OS=Homo sapiens GN=FCGBP PE=1 SV=3 30 18 O43866 CD5L_HUMAN CD5 antigen-like OS=Homo -
Research2007herschkowitzetvolume Al
Open Access Research2007HerschkowitzetVolume al. 8, Issue 5, Article R76 Identification of conserved gene expression features between comment murine mammary carcinoma models and human breast tumors Jason I Herschkowitz¤*†, Karl Simin¤‡, Victor J Weigman§, Igor Mikaelian¶, Jerry Usary*¥, Zhiyuan Hu*¥, Karen E Rasmussen*¥, Laundette P Jones#, Shahin Assefnia#, Subhashini Chandrasekharan¥, Michael G Backlund†, Yuzhi Yin#, Andrey I Khramtsov**, Roy Bastein††, John Quackenbush††, Robert I Glazer#, Powel H Brown‡‡, Jeffrey E Green§§, Levy Kopelovich, reviews Priscilla A Furth#, Juan P Palazzo, Olufunmilayo I Olopade, Philip S Bernard††, Gary A Churchill¶, Terry Van Dyke*¥ and Charles M Perou*¥ Addresses: *Lineberger Comprehensive Cancer Center. †Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. ‡Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA. reports §Department of Biology and Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. ¶The Jackson Laboratory, Bar Harbor, ME 04609, USA. ¥Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. #Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA. **Department of Pathology, University of Chicago, Chicago, IL 60637, USA. ††Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA. ‡‡Baylor College of Medicine, Houston, TX 77030, USA. §§Transgenic Oncogenesis Group, Laboratory of Cancer Biology and Genetics. Chemoprevention Agent Development Research Group, National Cancer Institute, Bethesda, MD 20892, USA. Department of Pathology, Thomas Jefferson University, Philadelphia, PA 19107, USA. Section of Hematology/Oncology, Department of Medicine, Committees on Genetics and Cancer Biology, University of Chicago, Chicago, IL 60637, USA. -
RAS FAMILY GTPASES INVOLVED in BREAST CANCER Ariella B
RAS FAMILY GTPASES INVOLVED IN BREAST CANCER Ariella B. Hanker A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Curriculum of Genetics and Molecular Biology. Chapel Hill 2009 Approved by: Channing J. Der (Advisor) Christopher Counter Adrienne Cox H. Shelton Earp Charles Perou ABSTRACT ARIELLA HANKER: Ras Family GTPases Involved in Breast Cancer (Under the direction of Channing J. Der) The Ras branch of the Ras superfamily of small GTPases consists of over thirty-six proteins that regulate a wide array of cellular processes. Mutations in the RAS oncogene that cause aberrant activation of Ras signaling drive 30% of all cancers, but these mutations are infrequent in breast cancer. Instead, other Ras family proteins may play more significant roles in the development and progression of breast cancer. Here, we focus on two such proteins, Rerg and Rheb. Hyperactive Rheb activity may enhance breast cancer tumorigenesis, whereas Rerg has been proposed to negatively regulate breast cancer growth. Expression of Rerg is controlled by estrogen; hence, Rerg is not expressed in ERα-negative breast cancers. Whether loss of Rerg expression in these tumors contributes to breast cancer progression is not known. We found that silencing Rerg expression did not significantly enhance the growth or invasive properties of breast cancer cells, and likewise, inducing Rerg expression in Rerg-negative breast cancer cell lines did not diminish their growth. Thus, these studies argue against a role for Rerg as a tumor suppressor in breast cancer. -
How Many Human Proteoforms Are There?
PERSPECTIVE PUBLISHED ONLINE: 14 FEBRUARY 2018 | DOI: 10.1038/NCHEMBIO.2576 How many human proteoforms are there? Ruedi Aebersold1, Jeffrey N Agar2, I Jonathan Amster3 , Mark S Baker4 , Carolyn R Bertozzi5, Emily S Boja6, Catherine E Costello7, Benjamin F Cravatt8 , Catherine Fenselau9, Benjamin A Garcia10, Ying Ge11,12, Jeremy Gunawardena13, Ronald C Hendrickson14, Paul J Hergenrother15, Christian G Huber16 , Alexander R Ivanov2, Ole N Jensen17, Michael C Jewett18, Neil L Kelleher19* , Laura L Kiessling20 , Nevan J Krogan21, Martin R Larsen17, Joseph A Loo22 , Rachel R Ogorzalek Loo22, Emma Lundberg23,24, Michael J MacCoss25, Parag Mallick5, Vamsi K Mootha13, Milan Mrksich18, Tom W Muir26, Steven M Patrie19, James J Pesavento27 , Sharon J Pitteri5 , Henry Rodriguez6, Alan Saghatelian28, Wendy Sandoval29, Hartmut Schlüter30 , Salvatore Sechi31, Sarah A Slavoff32, Lloyd M Smith12,33, Michael P Snyder24, Paul M Thomas19 , Mathias Uhlén34, Jennifer E Van Eyk35, Marc Vidal36, David R Walt37, Forest M White38, Evan R Williams39, Therese Wohlschlager16, Vicki H Wysocki40, Nathan A Yates41, Nicolas L Young42 & Bing Zhang42 Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous ques- tions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry–based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. -
Diagnostic Interpretation of Genetic Studies in Patients with Primary
AAAAI Work Group Report Diagnostic interpretation of genetic studies in patients with primary immunodeficiency diseases: A working group report of the Primary Immunodeficiency Diseases Committee of the American Academy of Allergy, Asthma & Immunology Ivan K. Chinn, MD,a,b Alice Y. Chan, MD, PhD,c Karin Chen, MD,d Janet Chou, MD,e,f Morna J. Dorsey, MD, MMSc,c Joud Hajjar, MD, MS,a,b Artemio M. Jongco III, MPH, MD, PhD,g,h,i Michael D. Keller, MD,j Lisa J. Kobrynski, MD, MPH,k Attila Kumanovics, MD,l Monica G. Lawrence, MD,m Jennifer W. Leiding, MD,n,o,p Patricia L. Lugar, MD,q Jordan S. Orange, MD, PhD,r,s Kiran Patel, MD,k Craig D. Platt, MD, PhD,e,f Jennifer M. Puck, MD,c Nikita Raje, MD,t,u Neil Romberg, MD,v,w Maria A. Slack, MD,x,y Kathleen E. Sullivan, MD, PhD,v,w Teresa K. Tarrant, MD,z Troy R. Torgerson, MD, PhD,aa,bb and Jolan E. Walter, MD, PhDn,o,cc Houston, Tex; San Francisco, Calif; Salt Lake City, Utah; Boston, Mass; Great Neck and Rochester, NY; Washington, DC; Atlanta, Ga; Rochester, Minn; Charlottesville, Va; St Petersburg, Fla; Durham, NC; Kansas City, Mo; Philadelphia, Pa; and Seattle, Wash AAAAI Position Statements,Work Group Reports, and Systematic Reviews are not to be considered to reflect current AAAAI standards or policy after five years from the date of publication. The statement below is not to be construed as dictating an exclusive course of action nor is it intended to replace the medical judgment of healthcare professionals. -
Positive Breast Cancer Cells by the Expression Profile of an Intrinsic Set
JOURNAL OF CELLULAR PHYSIOLOGY 200:440–450 (2004) Molecular Identification of ERa-Positive Breast Cancer Cells by the Expression Profile of an Intrinsic Set of Estrogen Regulated Genes ALESSANDRO WEISZ,1* WALTER BASILE,1 CLAUDIO SCAFOGLIO,1 LUCIA ALTUCCI,1 FRANCESCO BRESCIANI,1 ANGELO FACCHIANO,2 PIERO SISMONDI,3,4 LUIGI CICATIELLO,1 3,5 AND MICHELE DE BORTOLI 1Dipartimento di Patologia Generale, Seconda Universita` Degli Studi di Napoli, Vico L. De Crecchio 7, Napoli, Italy 2Istituto di Scienze dell’Alimentazione del Consiglio Nazionale delle Ricerche, Avellino, Italy 3IRCC-Institute for Cancer Research & Treatment, University of Turin, Candiolo (TO), Italy 4Department of Gynecology & Obstetrics, University of Turin, Candiolo (TO), Italy 5Department of Oncological Sciences, University of Turin, Candiolo (TO), Italy Estrogens exert a key biological role in mammary gland epithelial cells and promote breast carcinogenesis and tumor progression. We recently identified a new large set of estrogen responsive genes from breast cancer (BC) cells by DNA microarray analysis of the gene expression profiles induced by 17b-estradiol in ZR-75.1 and MCF-7 cells. The purpose of the present study was to test whether the expression pattern of hormone regulated genes from this set identifies estrogen receptor (ERa) positive, hormone responsive BC cells. To this aim, we carried out in silico metanalysis of ERa positive and ERa negative human BC cell line transcriptomes, focusing on two sets of 171 and 218 estrogen responsive genes, respectively. Results show that estrogen dependent gene activity in hormone responsive BC cells is significantly different from that of non-responsive cells and, alone, allows to discriminate these two cellular phenotypes.